Abstract The nematode C. elegans is unique among model organisms in having a defined lineage and known connections for all its 302 neurons. The genome sequence was completed more than 20 years ago, but knowing which genes in the genome are used in exactly which cells and what transcription factors are controlling that expression remains a major challenge. We have successfully applied single cell- (sc-)RNA-seq methods to one larval stage and three embryonic stages to measure the RNA content of individual cells across the whole animal. We also have preliminary data that indicates that we can assay chromatin accessibility at the single cell level using the assay for transposase accessible chromatin (ATAC-seq). We now propose to collect both sc-RNA-seq and ATAC-seq data at multiple stages to determine the gene expression patterns of each cell in the worm and the active regulatory sequence throughout the entire life cycle of C. elegans. In turn we will use the combined data sets along with chromatin- immunoprecipitation- (ChIP-) seq data to impute what transcription factors are controlling expression of each gene in the genome in every cell and what regulatory sequences these transcription factors recognize. The results will provide a valuable resource to scientists studying the worm and addresses a major outstanding question in the molecular biology of development. In addition, these data sets, from an animal with a ?ground truth? should serve as a platform for methods development in the single cell field.